Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000204645.1:WP_013518270.1 Length = 398 Score = 202 bits (513), Expect = 2e-56 Identities = 137/418 (32%), Positives = 217/418 (51%), Gaps = 49/418 (11%) Query: 36 LPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF 95 +PI +ERG+G+RV+DV+G + D G+ V +GH+HPR+V A+++Q K H T + Sbjct: 19 VPIALERGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPALQEQIAKLIH---TSNY 75 Query: 96 YENAIILAEKLIELAPGDIER-KVVYGNSGAEANEAAMKLV-KYGTGR----KQFLAFYH 149 Y + E+L L G + N+G EANE A+K+ KYG + + + + H Sbjct: 76 YH--VPGQEELARLLTGRARMTNAFFCNTGLEANECAIKIARKYGVDKGIEKPEIVVYDH 133 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 AFHGR+ A ++ T + V+ +GF P + G + PN I+ +E E V+ Sbjct: 134 AFHGRSIATMTATGNPKVR-NGFGPLLEGFIRVA-PND------IEALQEATEGNPNVV- 184 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 A+ EPIQGEGG + + ++K D G LL DEVQ G+ Sbjct: 185 ----------------AVLMEPIQGEGGLHPMRVEYLQQVRKLCDANGWLLMLDEVQAGM 228 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVI-HRADITFDKPGRHATTFGGNPVAI 328 GRTGK++A + G+ PD++ K +G G+P+ V+ H A KPG H +TFGGNP+A+ Sbjct: 229 GRTGKWFAHQWAGIVPDVMTLAKGLGSGVPVGAVLAHGAASEVLKPGNHGSTFGGNPLAM 288 Query: 329 AAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKET 386 AG+E + I++E LL + +VG +L L++ + + RG GL VE+ + Sbjct: 289 RAGVETIRIMEEEGLLQNAADVGAHLKAGLQQALGSVPGVNEVRGQGLIIGVELDRPCGV 348 Query: 387 KEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALKAAL 444 ++ +A+ GL+L D IR +P L +T+ E D + + ++A L Sbjct: 349 ----------LIDRAAQAGLLLSVTADRVIRLVPALTLTRAEADEIVALLTPLVQAFL 396 Lambda K H 0.320 0.141 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 493 Number of extensions: 25 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 398 Length adjustment: 32 Effective length of query: 413 Effective length of database: 366 Effective search space: 151158 Effective search space used: 151158 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory